Need Help designing a workflow

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3.5 years ago

ZBL • 0

Hello!

I'm very new here, and was forced to shift to writing a bioinformatics dissertation because almost all the wet-labs in my country are closed. I am absolutely clueless about how this works and am still studying basic Python/R in the mean time. That being said, I need help designing a workflow for the specific reason of comparing resistance gene abundance between multiple samples of soil.

Would bowtie2 or blastn be more suitable for my needs? Would I need to assemble the data from the Illumina sequencer before alignment?

Many Thanks,

Zach

alignment sequencing resistomes ARG • 573 views

ADD COMMENT • link 3.5 years ago by ZBL • 0

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Have you found any papers describing what you want to do?

ADD REPLY • link 3.5 years ago by swbarnes2 14k

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Thank you for your response! I have been reading papers for the past few weeks and some have similar goals although really just differ in the assembly or alignment tools used respectively. I apologize if I seem unknowledgeable.

ADD REPLY • link 3.5 years ago by ZBL • 0

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